{"entity": "researcher", "timestamp": "2026-08-13T18:59:16.623Z", "family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "affiliations": ["Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0"}}, "publications": [{"entity": "publication", "iuid": "8ed54f29f33f4ce39d346fdb35295c92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ed54f29f33f4ce39d346fdb35295c92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ed54f29f33f4ce39d346fdb35295c92"}}, "title": "Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.", "authors": [{"family": "Prast-Nielsen", "given": "Stefanie", "initials": "S", "orcid": "0000-0001-5877-7988", "researcher": {"href": "https://publications.scilifelab.se/researcher/baea894b3ac14408a7492df2fc6c796e.json"}}, {"family": "Granstr\u00f6m", "given": "Anna L\u00f6f", "initials": "AL", "orcid": "0000-0003-2169-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c08d2119eca4e67936cd5b5d2dc47d3.json"}}, {"family": "Kiasat", "given": "Ali", "initials": "A", "orcid": "0000-0001-5568-3265", "researcher": {"href": "https://publications.scilifelab.se/researcher/f92cb577648943a2a09efe76787545c4.json"}}, {"family": "Ahlstr\u00f6m", "given": "Gustav", "initials": "G"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/6538b950bbd440e3aa32435d23c98074.json"}}, {"family": "Rautiainen", "given": "Susanne", "initials": "S", "orcid": "0000-0001-7193-6082", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb22af02cdd04e80b1a0809b163ad56e.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Andersson", "given": "Fredrik O", "initials": "FO"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications.scilifelab.se/researcher/17bed8be7a9c46b5a94147b80fd58e82.json"}}, {"family": "Gustafsson", "given": "Ulf O", "initials": "UO", "orcid": "0000-0001-9549-061X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4302890c32a24317aa1d0f6807c4458e.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "35039", "issn-l": "2045-2322"}, "abstract": "Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.", "doi": "10.1038/s41598-025-18106-7", "pmid": "41062543", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12508173"}, {"db": "pii", "key": "10.1038/s41598-025-18106-7"}], "notes": [], "created": "2025-11-07T15:05:48.239Z", "modified": "2025-11-07T15:05:53.602Z"}, {"entity": "publication", "iuid": "bdd145617e0c401ea708379b0493f458", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdd145617e0c401ea708379b0493f458.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdd145617e0c401ea708379b0493f458"}}, "title": "Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden.", "authors": [{"family": "T\u00e5ng Hallb\u00e4ck", "given": "Erika", "initials": "E"}, {"family": "Bj\u00f6rkman", "given": "Jonas T", "initials": "JT"}, {"family": "Dyrkell", "given": "Fredrik", "initials": "F"}, {"family": "Welander", "given": "Jenny", "initials": "J"}, {"family": "Fang", "given": "Hong", "initials": "H"}, {"family": "Sylvin", "given": "Isak", "initials": "I"}, {"family": "Kaden", "given": "Ren", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications.scilifelab.se/researcher/018870b1d0034ee09552a3ae451d5504.json"}}, {"family": "Eilers", "given": "Hinnerk", "initials": "H"}, {"family": "S\u00f6derlund Strand", "given": "Anna", "initials": "A"}, {"family": "Mernelius", "given": "Sara", "initials": "S"}, {"family": "Berglind", "given": "Linda", "initials": "L"}, {"family": "Campillay Lagos", "given": "Amaya", "initials": "A"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}, {"family": "Sikora", "given": "Per", "initials": "P", "orcid": "0000-0002-0049-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaccd4a7ab4105be077ee778cf0507.json"}}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "11", "issue": "1", "issn-l": null}, "abstract": "Background. National epidemiological investigations of microbial infections greatly benefit from the increased information gained by whole-genome sequencing (WGS) in combination with standardized approaches for data sharing and analysis.Aim. To evaluate the quality and accuracy of WGS data generated by different laboratories but analysed by joint pipelines to reach a national surveillance approach.Methods. A national methicillin-resistant Staphylococcus aureus (MRSA) collection of 20 strains was distributed to nine participating laboratories that performed in-house procedures for WGS. Raw data were shared and analysed by three pipelines: 1928 Diagnostics, JASEN (GMS pipeline) and CLC-Genomics Workbench. The outcomes were compared according to quality, correct strain identification and genetic distances.Results. One isolate contained intraspecies contamination and was excluded from further analysis. The mean sequencing depth varied between sites and technologies. However, all analysis methods identified 12 strains that belonged to one of five outbreak clusters. The cut-off definition was set to <10 allele differences for core genome multilocus sequence typing (cgMLST) and <20 genetic differences for SNP analysis in a pairwise comparison.Conclusions. MRSA isolates, which are whole genome sequenced by different laboratories and analysed using the same bioinformatic pipelines, yielded comparable results for outbreak clustering for both cgMLST and SNP, using the 1928 analysis pipeline. In this study, JASEN was best suited to analyse Illumina data and CLC to analyse within respective technology. In the future, real-time sharing of data and harmonized analysis within the Genomic Medicine Sweden consortium will further facilitate investigations of outbreaks and transmission routes.", "doi": "10.1099/mgen.0.001331", "pmid": "39869391", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative", "Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11893271"}], "notes": [], "created": "2025-03-19T04:58:38.247Z", "modified": "2025-11-19T15:18:20.002Z"}, {"entity": "publication", "iuid": "9f8d979842f84159b0af3300d9959528", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f8d979842f84159b0af3300d9959528.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f8d979842f84159b0af3300d9959528"}}, "title": "Building a precision medicine infrastructure at a national level: The Swedish experience", "authors": [{"family": "Edsj\u00f6", "given": "Anders", "initials": "A", "orcid": "0000-0001-8783-8284", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fae25d88855440194b9bb11b3d18bf8.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Gisselsson", "given": "David", "initials": "D", "orcid": "0000-0002-0301-426X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3653582762b14f9a9ad2fe6aba511115.json"}}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Friedman", "given": "Mikaela", "initials": "M", "orcid": "0000-0002-5483-9771", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1507c81499748d8bf0ee1eb647a37d4.json"}}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Johansson", "given": "Maria", "initials": "M"}, {"family": "Ehrencrona", "given": "Hans", "initials": "H", "orcid": "0000-0002-5589-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b89608a8ce941c3b9911630b4ff9720.json"}}, {"family": "Fagerqvist", "given": "Therese", "initials": "T"}, {"family": "Strid", "given": "Tobias", "initials": "T", "orcid": "0000-0002-2166-5170", "researcher": {"href": "https://publications.scilifelab.se/researcher/8294f89150574803a12bc1944714d12b.json"}}, {"family": "Lovmar", "given": "Lovisa", "initials": "L"}, {"family": "Jacobsson", "given": "Bo", "initials": "B", "orcid": "0000-0001-5079-2374", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd6968816ded4a50b1029ee3f4afbeed.json"}}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}, {"family": "Wheelock", "given": "Craig E", "initials": "CE", "orcid": "0000-0002-8113-0653", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3cd2b99e3e9486ba41030c809a48c51.json"}}, {"family": "Sikora", "given": "Per", "initials": "P", "orcid": "0000-0002-0049-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaccd4a7ab4105be077ee778cf0507.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}], "type": "journal-article", "published": "2023-00-00", "journal": {"title": "Camb. prisms Precis. med.", "issn": "2752-6143", "issn-l": null, "volume": "1", "issue": null, "pages": null}, "abstract": null, "doi": "10.1017/pcm.2023.3", "pmid": "38550923", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-11-30T22:32:34.264Z", "modified": "2025-12-03T11:34:03.536Z"}, {"entity": "publication", "iuid": "ef398bc7e3dd48a38a05d94d36cd4787", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef398bc7e3dd48a38a05d94d36cd4787.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef398bc7e3dd48a38a05d94d36cd4787"}}, "title": "Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.", "authors": [{"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F", "orcid": "0000-0003-0173-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/49d15be15c484e6a99f22b466bf99166.json"}}, {"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications.scilifelab.se/researcher/badb913f91e14489aca247ee841e1608.json"}}, {"family": "Gonzales-Siles", "given": "Lucia", "initials": "L"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Sikora", "given": "Per", "initials": "P", "orcid": "0000-0002-0049-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaccd4a7ab4105be077ee778cf0507.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Moore", "given": "Edward R B", "initials": "ERB"}], "type": "journal article", "published": "2016-06-16", "journal": {"title": "Genome Announc", "issn": "2169-8287", "issn-l": "2169-8287", "volume": "4", "issue": "3", "pages": "e00552-16"}, "abstract": "Moraxella catarrhalis is a Gram-negative commensal and pathogenic bacterium found in the human respiratory tract. It is associated with otitis media and respiratory tract infections. Here, we report the draft genome sequence of M. catarrhalis type strain CCUG 353(T), composed of 18 contigs and a total size of 1.89 Mb.", "doi": "10.1128/genomeA.00552-16", "pmid": "27313296", "labels": {"National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "4/3/e00552-16"}, {"db": "pmc", "key": "PMC4911475"}], "notes": [], "created": "2017-05-08T07:58:54.487Z", "modified": "2023-05-15T16:46:23.175Z"}]}